The Quantum chemical cluster approach has been shown to be quite powerful and efficient in the modeling of enzyme active sites and reaction mechanisms. In this thesis, the reaction mechanisms of several enzymes have been investigated using the hybrid density functional B3LYP. The enzymes studied include four dinuclear zinc enzymes, namely dihydroorotase, N-acyl-homoserine lactone hydrolase, RNase Z, and human renal dipeptidase, two trinuclear zinc enzymes, namely phospholipase C and nuclease P1, two tungstoenzymes, namely formaldehyde ferredoxin oxidoreductase and acetylene hydratase, aspartate α-decarboxylase, and mycolic acid cyclopropane synthase. The potential energy profiles for various mechanistic scenarios have been calculated and analyzed. The role of the metal ions as well as important active site residues has been discussed.   In the cluster approach, the effects of the parts of the enzyme that are not explicitly included in the model are taken into account using implicit solvation methods.   For all six zinc-dependent enzymes studied, the di-zinc bridging hydroxide has been shown to be capable of performing nucleophilic attack on the substrate. In addition, one, two, or even all three zinc ions participate in the stabilization of the negative charge in the transition states and intermediates, thereby lowering the barriers.   For the two tungstoenzymes, several different mechanistic scenarios have been considered to identify the energetically most feasible one. For both enzymes, new mechanisms are proposed.   Finally, the mechanism of mycolic acid cyclopropane synthase has been shown to be a direct methyl transfer to the substrate double bond, followed by proton transfer to the bicarbonate.   From the studies of these enzymes, we demonstrate that density functional calculations are able to solve mechanistic problems related to enzymatic reactions, and a wealth of new insight can be obtained.

Made available in DSpace on 2015-05-14T13:21:30Z (GMT). No. of bitstreams: 1 arquivototal.pdf: 4538639 bytes, checksum: 981ce0eef0681003af97d1a8046c66ee (MD5) Previous issue date: 2013-08-06 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / The aim of this work was to study two kinds of intermolecular hydrogen bonding, the non-usual that is represented by the interaction between acetylene and the HX species (C2H2 --- HX) and the usual that is represented by the interaction between hydrogen cyanide and HX species, with X = F, Cl, CN, and HCCH. This interaction promotes changes in the structural, electronic and vibrational properties of the species involved. In this work, we employe d not onlycomputational-quantum methods MP2/6-311 + + G (d, p) and DFT/B3LYP/6-311 + + G (d, p) in order to study the structural, electronic and vibrational properties of those two types of intermolecular hydrogen bonding, but also we employed QTAIM and NBO methods to complement our research. The results have shown no significant differences between the two correlated methods employed for both types of hydrogen bonded complexes, leading us to suggest the use of the DFT/B3LYP method for studies of similar systems to those studied here, due to the lower computational demand. The increase in bond length of the HX species are enhanced due to formation of more linear complexes than T-complexes, in both calculation levels. The intermolecular bond length values in the complex HCN --- HX are smaller than in the complexes HCCH --- HX, and the values from MP2 and DFT/B3LYP are very close in each individual type of hydrogen complex, suggesting that the linear complexes are more stabilized by the formation of hydrogen bonding than the T-complexes, which can be proved by the values of the binding energy of hydrogen in HCN --- HX. Concerning the redshift effect in the harmonic vibrational mode of species HX, due to the formation of intermolecular bond, the values obtained for linear complexes hydrogen are higher than for the corresponding T-complexes, considering both calculation levels. Values were evaluated from the increase in the intensity values of the stretch mode HX bond formation due to intermolecular and, according to the model CCFOM, the term load flow is responsible for the effect on the increase of HX intensity. We also highlight the new vibrational modes, emphasizing the stretch mode of the intermolecular bond. From studies employing QTAIM, it was possible to obtain the values of electron density and the Laplacian electron density and evaluate these parameters in critical points in HX and intermolecular hydrogen bonding, thus confirming the formation of hydrogen bonded complexes. We evaluated the energy difference between π orbitals and lone pair of nitrogen (in HCN), for the species receiving proton and sigma antibonding for the hydrogen of HX, using the method of natural bond orbital variation. / O objeto de estudo deste trabalho foi a ligação de hidrogênio intermolecular de dois tipos, a não-usual representada pela interação entre o acetileno e espécies HX (C2H2---HX) e a usual representada pela interação entre o ácido cianídrico e espécies HX, com X=F, Cl, CN e HCCH. Esta interação provoca mudanças nas propriedades estruturais, eletrônicas e vibracionais das espécies envolvidas. Neste trabalho empregamos os métodos quântico-computacionais MP2/6-311++G(d,p) e DFT/B3LYP/6-311++G(d,p) para estudar as propriedades estruturais, eletrônicas e vibracionais dos dois tipos de ligação de hidrogênio intermolecular, além de complementar nossa investigação empregando os métodos QTAIM e NBO. Os resultados não mostraram diferenças significativas entre os dois métodos correlacionados empregados para ambos os tipos de complexos de hidrogênio, nos levando a sugerir o emprego do método DFT/B3LYP para estudos de sistemas semelhantes aos aqui estudados, devido a menor demanda computacional. Os valores de incremento no comprimento de ligação das espécies HX são mais acentuados devido à formação dos complexos lineares do que dos complexos-T, em ambos os níveis de cálculo. Os valores de comprimento de ligação intermolecular nos complexos HCN---HX são menores do que nos complexos HCCH---HX, sendo os valores MP2 e DFT/B3LYP bem próximos em cada tipo individual de complexo de hidrogênio, sugerindo que os complexos lineares são mais estabilizados pela formação da ligação de hidrogênio do que os complexos-T, fato que pode ser comprovado pelos valores da energia de ligação de hidrogênio em HCN---HX. Com respeito ao efeito redshift no modo vibracional harmônico das espécies HX, devido à formação da ligação intermolecular, os valores obtidos para os complexos de hidrogênio lineares são maiores do que para os correspondentes complexos-T, considerando ambos os níveis de cálculo. Foram avaliados os valores do incremento nos valores de intensidade do modo de estiramento de HX devido à formação da ligação intermolecular e, de acordo com o modelo CCFOM, o termo de fluxo de carga é o responsável pelo efeito no aumento da intensidade de HX. Foram ainda destacados os novos modos vibracionais, dando ênfase ao modo de estiramento da ligação intermolecular. Dos estudos empregando a QTAIM foi possível obter os valores da densidade eletrônica e do Laplaciano da densidade eletrônica e avaliar os valores desses parâmetros nos pontos críticos de ligação em HX e na ligação de hidrogênio intermolecular, comprovando dessa forma a formação dos complexos de hidrogênio. Com os estudos empregando o método dos orbitais naturais de ligação foi avaliada a diferença de energia entre os orbitais π (no acetileno) e o orbital do par de elétrons livres do nitrogênio (em HCN), para as espécies receptoras de próton, e o orbital sigma antiligante do hidrogênio em HX.

Perfluorinated sulfonic acid (PFSA) ionomer membranes demonstrate great potential for use in proton exchange membrane fuel cells (PEMFCs) due to their favorable electronic properties and excellent efficiency. However, the assignment of key vibrational transitions such as the symmetric sulfonate and ether stretches is not yet fully understood depriving researchers of a quick and simple technique for analyzing morphological changes. The symmetric sulfonate stretch could be used to track changes in the ionic clusters formed within the membrane while the ether stretch will provide insight into the largely semi-crystalline PTFE phase. Alterations in either regime will affect both ion transport and mechanical properties and produce a major shift in device performance. This study focused on predicting the vibrational transitions for Aquivion, 3M PFSA, and Nafion using density functional theory (DFT) with the bulk being performed using the same functional and basis set combination, B3LPY/6-31+G*. For all three ionomers, the predicted vibrational transitions were affected by changes in both the conformer and solvation method with water being used as the solvent. Despite the noted changes, both vibrational transitions were determined to be within the range of 970-1100 cm-1 with the symmetric sulfonate stretch present at around 970-1010 cm-1 and the ether stretch observed at around 1050-1100 cm-1 with solvation present. While the calculated peak positions mirror those found in the experimental spectra within the literature, the traditional normal mode assignments do not match those predicted by our calculations. However, recent studies have hypothesized that these vibrational transitions are coupled, which could explain why they have been so difficult to assign. / Master of Science / Perfluorinated sulfonic acid (PFSA) ionomer membranes show great promise for use in proton exchange membrane fuel cells (PEMFCs) due to their excellent efficiency. However, the current techniques used to determine changes in structural configurations require sophisticated equipment and trained personnel to operate. Simpler techniques exist wherein the vibrations of certain bonds can be measured upon exposure of the sample to measured amounts of infrared light. The problem with this technique is that researchers currently do not fully understand at what wavelengths certain portions of the polymer known as functional groups will vibrate. These vibrations are also known as vibrational transitions. This study was undertaken to predict through numerical solutions to the Schrödinger equation at what wavelengths two particular vibrational transitions would occur for three common ionomers, Aquivion, 3M PFSA, and Nafion. For all three structures, the positions of these transitions mirrored that observed within the literature although the functional groups assigned to these positions did not match with those identified by our calculations. However, recent studies have indicated that these vibrational transitions occur at the same positions, which could explain why they have been so difficult to assign.

Made available in DSpace on 2017-07-24T19:37:53Z (GMT). No. of bitstreams: 1 Luis Lacerda.pdf: 6157407 bytes, checksum: 67f47ee9ce5d908521ba3d0455add580 (MD5) Previous issue date: 2015-03-09 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Semiconductors materials are largely employed on development of innumerous optical and electronic due to their electronic, optical, ferroelectric and structural properties. Among the semiconductors materials stand out the zinc oxide (ZnO) and the barium titanate (BaTiO3) once shows excellent properties allied to low cost to obtaining. The ZnO is a simple oxide used in technology and largely investigated as an alternative to replace high cost material on development of electronic devices. Similarly, the BaTiO3 has perovskite crystalline structure whose properties present great technological interest. This work evaluated the effect of Ba presence on wurtzite structure and the influence of Zn atoms on tetragonal BaTiO3 properties. The obtained results indicates that the Ba atoms changes drastically the band structure of ZnO, resulting in the decrease of band gap for low quantities and the semiconductor type modification for doping above 25 %. The insertion of such atoms in wurtzite also causes the improvement of ferroelectric properties and the increase of unit cell lattice parameters. In case of Zn-doped BaTiO3, the doping process reduces radically de band gap and the ferroelectric properties regarding to pure material. Likewise, the semiconductor type is also modified by the Zn atoms presence. Based on obtained results for both crystalline systems, was proposed their employed in formation of p-n heterojunction. The heterostructure was evaluated through of four models. The obtained results for each one of these models were used to describe the interface region of ZnO/BaTiO3 heterojunction, proving that the atoms intercalation occurs and is responsible for heterostructure properties. Such properties present this heterostructure as a potential alternative for development of electronic devices, mainly the development of memory devices. The obtained heterostructure requires a low amount energy to electronic conduction process and shows high compatibility between the structure of heterojunction and the SiO2 substrate which is used in development of such devices. / Materiais semicondutores são amplamente empregados no desenvolvimento de vários dispositivos ópticos e eletrônicos variados devido às suas propriedades eletrônicas, ópticas, ferroelétricas e estruturais. Dentre os materiais semicondutores, destacam-se o óxido de zinco (ZnO) e o Titanato de Bário (BaTiO3) uma vez que apresentam excelentes propriedades aliadas ao baixo custo de síntese. O ZnO é um óxido simples amplamente empregado na tecnologia e largamente investigado como uma alternativa para substituição de materiais de custo elevado no desenvolvimento de dispositivos eletrônicos. Por sua vez, o BaTiO3 é um material de estrutura cristalina perovskita cujas propriedades são de grande interesse tecnológico. No presente trabalho avaliou-se o efeito da presença de átomos de Ba na estrutura wurtzita do ZnO e a influência dos átomos de Zn sobre as propriedades do BaTiO3 tetragonal. Os resultados indicaram que os átomos de bário alteram drasticamente a estrutura de bandas do ZnO, resultando na diminuição do band gap para pequenas quantidades e a modificação do tipo de semicondutor para dopagens superiores a 25%. A inserção de tais átomos na estrutura wurtzita também é responsável pelo aprimoramento das propriedades ferroelétricas do material, bem como pelo aumento dos parâmetros de rede da célula unitária. No caso da estrutura do BaTiO3 dopada com Zn observou-se a redução drástica do band gap para o material e a modificação do caráter semicondutor do material; entretanto, ocorreu a redução das propriedades ferroelétricas em relação ao BaTiO3 puro. Com base nos resultados obtidos para ambos os sistemas cristalinos, propôs-se a sua utilização para formação de uma heterojunção do tipo p-n. A heteroestrutura foi avaliada por meio de quatro modelos diferentes. Os resultados obtidos para cada um destes modelos foram utilizados para descrição da estrutura eletrônica da região de interface da heterojunção, comprovando que a intercalação de átomos na interface é observada e mostra-se responsável pelas propriedades observadas para a heteroestrutura. Tais propriedades apontam a heterojunção ZnO/BaTiO3 como uma alternativa em potencial para aplicação no desenvolvimento de dispositivos eletrônicos e, principalmente, no desenvolvimento de dispositivos de armazenamento de dados, devido a diminuição de energia necessária para condução eletrônica.

Made available in DSpace on 2017-07-24T19:38:09Z (GMT). No. of bitstreams: 1 DaniellaIngles.pdf: 4512280 bytes, checksum: c8619d3eba91fdbec4d26eeb30e24eb9 (MD5) Previous issue date: 2013-03-08 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior / Titanates have perovskite crystalline structure very known for electrical and optical properties used in the electronic devices such as sensors, capacitors, nonvolatile and dynamic random access memories. In particular, titanates structures are characterized for the ABO3 formula being A crystallographic site formed by 12 atoms neighbors and B crystallographic site formed by 6 atoms neighbors. However, researches about strontium titanate-stannate system are found minimally in the literature. Articles discussing synthesis, characterization and compositions are insufficiently presented. This project shows a theoretical study of the structure and optical properties of the strontium titanate-stannate system for different substitutions [Sr(Ti1-xSnx)O3 x = 0; 0,25; 0,50; 0,75; 1]. It was used theoretical-computational methodology based on, Density Functional Theory (DFT) with B3LYP functional to calculate the structure of the models SrTiO3 (STO), Sr(Ti1-xSnx)O3 (STS) and SrSnO3 (SSO). Theoretical data of parameter lattice, cell unit angles, volume, band gap, overlap population, charges and free energy are presented as well as analysis and discussion of the results for band structure (EB), density of states (DOS), electron density maps. Thus, one may present the data obtained and investigate the properties of the materials. / Titanatos possuem estrutura cristalina perovskita muito conhecida pelas propriedades elétricas e ópticas utilizadas em dispositivos eletrônicos como sensores, capacitores, memória de acesso randômico dinâmica e não volátil. Em particular, as estruturas de titanatos são caracterizadas pela fórmula ABO3 sendo A sítio cristalográfico formado por 12 átomos vizinhos e B o sítio cristalográfico formado por 6 átomos vizinhos. No entanto, pesquisas sobre o sistema titanato-estanato de estrôncio são encontradas minimamente na literatura. Artigos que discutem a síntese, caracterização e composições são insuficientemente apresentados. Este trabalho apresenta o estudo teórico da estrutura e propriedades ópticas do sistema titanato-estanato de estrôncio para diferentes substituições [Sr(Ti1-xSnx)O3 x = 0; 0,25; 0,50; 0,75; 1]. Utilizou-se metodologia teórico-computacional baseada em, Teoria do Funcional de Densidade (DFT) com funcional B3LYP, para cálculo da estrutura dos modelos SrTiO3 (STO), Sr(Ti1-xSnx)O3 (STS) e SrSnO3 (SSO). Dados teóricos de parâmetro de rede, ângulos da célula unitária, band gap, recobrimento populacional, cargas e energia livre são apresentados como também a análise e discussão dos resultados por meio de estrutura de bandas (EB), densidade de estados (DOS), mapas de densidade eletrônica. Desta forma, podem-se apresentar os dados obtidos e investigar as propriedades dos materiais.

Ce travail présente une étude théorique des spectres RMN de molécules biologiques. Dans la première partie, les calculs DFT des paramètres RMN (déplacements chimiques et constantes de couplage spin-spin) pour les protons liés à des atomes de carbone ont été réalisés pour quatre métabolites de la prostate: la putrescine, la spermidine, la spermine, et la sarcosine, et trois métabolites du cerveau: l'acétate, l'alanine et la sérine. Une étude théorique systématique, dans l'approche DFT, des paramètres de RMN des métabolites a montré que la méthode B3LYP/6-311++G** est un bon compromis entre la précision et les coûts. Les contributions du solvant ont été évaluées en utilisant le modèle PCM, les effets des isomères, pondérés dans l’approximation de Boltzmann, ont été pris en compte, et les corrections de vibration de point zéro ont été estimées en utilisant une approche perturbative au second ordre. La comparaison avec l'expérience a démontré que tous ces effets sont nécessaires pour améliorer l'accord entre les données calculées et expérimentales, aboutissant à des résultats de grande précision. Dans la deuxième partie, nous avons développé un nouveau modèle, BioShift, qui permet la prédiction des déplacements chimiques des différents noyaux (H, N, C ...) pour des molécules biologiques (protéines, ADN, ARN, polyamine ...). Il est simple, rapide, et comporte un nombre limité de paramètres. La comparaison avec des modèles sophistiqués conçus spécialement pour la prédiction des déplacements chimiques des protéines a montré que Bioshift est concurrentiel avec de tels modèles. / The present work presents a theoretical study of the NMR spectra of biological molecules. In the first part, DFT calculations of the spin-Hamiltonian NMR parameters (chemical shifts and spin-spin coupling constants) for protons attached to carbon atoms have been performed for four prostate metabolites: putrescine, spermidine, spermine, and sarcosine, and three brain metabolites: acetate, alanine, and serine. A theoretical investigation, within the DFT approach, of the NMR parameters of metabolites has shown that the B3LYP/6-311++G** level of calculation is a good compromise between accuracy and costs. Contributions from solvent were evaluated using the PCM model, Boltzmann weighted isomer effects were calculated, and zero-point vibrational corrections were estimated using a second order perturbation approach. Comparison with experiment has demonstrated that all these effects are necessary to improve the agreement between calculated and experimental data. In the second part, we have presented a new model, BioShift, that allows the prediction of chemical shifts of different nuclei (H, N, C…) for biological molecules (proteins, DNA, RNA, polyamine …). It is simple, fast, and involves a limited number of parameters. Comparison with well-known sophisticated models designed especially for the prediction of chemical shifts of proteins showed that Bioshift is competitive with such models.

The possibility of using methylamines instead of ammonia as a nitrogen precursor for the CVD of nitrides is studied using quantum chemical computations of reaction energies: reaction electronic energy (Δ𝑟𝐸𝑒𝑙𝑒𝑐) reaction enthalpy (Δ𝑟𝐻) and reaction free energy (Δ𝑟𝐺). The reaction energies were calculated for three types of reactions: Uni- and bimolecular decomposition to more reactive nitrogen species, adduct forming with trimethylgallium (TMG) and trimethylaluminum (TMA) followed by a release of methane or ethane and surface adsorption to gallium nitride for both the unreacted ammonia or methylamines or the decomposition products. The calculations for the reaction entropy and free energy were made at both STP and CVD conditions (300°C-1300°C and 50 mbar). The ab inito Gaussian 4 (G4) theory were used for the calculations of the decomposition and adduct reactions while the surface adsorptions were calculated using the Density Functional Theory method B3LYP. From the reactions energies it can be concluded that the decomposition was facilitated by the increasing number of methyl groups on the nitrogen. The adducts with mono- and dimethylamine were more favorable than ammonia and trimethylamine. 𝑁𝐻2 was found to be most readily to adsorb to 𝐺𝑎𝑁 while the undecomposed ammonia and methylamines was not willingly to adsorb.

Ce travail présente une étude théorique des spectres RMN de molécules biologiques. Dans la première partie, les calculs DFT des paramètres RMN (déplacements chimiques et constantes de couplage spin-spin) pour les protons liés à des atomes de carbone ont été réalisés pour quatre métabolites de la prostate: la putrescine, la spermidine, la spermine, et la sarcosine, et trois métabolites du cerveau: l'acétate, l'alanine et la sérine. Une étude théorique systématique, dans l'approche DFT, des paramètres de RMN des métabolites a montré que la méthode B3LYP/6-311++G** est un bon compromis entre la précision et les coûts. Les contributions du solvant ont été évaluées en utilisant le modèle PCM, les effets des isomères, pondérés dans l'approximation de Boltzmann, ont été pris en compte, et les corrections de vibration de point zéro ont été estimées en utilisant une approche perturbative au second ordre. La comparaison avec l'expérience a démontré que tous ces effets sont nécessaires pour améliorer l'accord entre les données calculées et expérimentales, aboutissant à des résultats de grande précision. Dans la deuxième partie, nous avons développé un nouveau modèle, BioShift, qui permet la prédiction des déplacements chimiques des différents noyaux (H, N, C ...) pour des molécules biologiques (protéines, ADN, ARN, polyamine ...). Il est simple, rapide, et comporte un nombre limité de paramètres. La comparaison avec des modèles sophistiqués conçus spécialement pour la prédiction des déplacements chimiques des protéines a montré que Bioshift est concurrentiel avec de tels modèles.

Numerical methods are often required to solve chemical problems, either to verify theoretical models or to access information that is not readily available experimentally. This thesis deals with both situations, though in differing levels of detail. A major component of this thesis is devoted to developing new methods to determine a full eigendecomposition of the matrices derived from "low temperature" unimolecular master equations. When transient behaviour is of interest achieving relative accuracy for more than just the eigenvector corresponding to the smallest eigenvalue is of central importance. Three new methods are presented. The first is based on a weighted implementation of subspace projection methods, in this case explored for the well-known Arnoldi method. This weighted inner product subspace projection methodology is demonstrated to

Numerical methods are often required to solve chemical problems, either to verify theoretical models or to access information that is not readily available experimentally. This thesis deals with both situations, though in differing levels of detail. A major component of this thesis is devoted to developing new methods to determine a full eigendecomposition of the matrices derived from "low temperature" unimolecular master equations. When transient behaviour is of interest achieving relative accuracy for more than just the eigenvector corresponding to the smallest eigenvalue is of central importance. Three new methods are presented. The first is based on a weighted implementation of subspace projection methods, in this case explored for the well-known Arnoldi method. This weighted inner product subspace projection methodology is demonstrated to